Analysis
Seraphina Shi
Linear regression
In the following section, we performed traditional linear regression with equation \[Y = \beta_0 + \beta_1 *X\] where \(Y\) is one of the epigenetic age accelerations, and \(X\) is one of the ambient exposure measurements or the urinary measurements.
The estimations of \(\beta_1\) with given \(Y\) and \(X\) are shown below, which can be interpreted as “the mean of Y changes given a one-unit increase in X while holding other variables constant”.
Ambient Exposure
## X: Ambient Exposure Measurements:## bap pm25
## Horvath EAA -0.0068 (0.0048) 0.0018 (0.0024)
## Hannum EAA -0.0019 (0.0042) 0.0001 (0.002 )
## PhenoAge EAA -0.0031 (0.0046) -0.0013 (0.0022)
## Skin&Blood EAA 0.0028 (0.0034) -0.0006 (0.0017)
## GrimAge EAA 0.0017 (0.0031) 0.0013 (0.0015)
## DNAmTL 0 (0.0002) -0.0001 (0.0001)
## IEAA -0.0097* (0.0042) 0.0015 (0.0022)
## EEAA -0.0004 (0.0054) 0.0005 (0.0026)
## [P<0.001: ***; P<0.01: **; P<0.05: *] <NA>
## ANY BPE BaA
## Horvath EAA 0.0009 ** (0.0003) -0.007 (0.0046) -0.0041 (0.0029)
## Hannum EAA 0.0004 (0.0003) -0.0026 (0.004 ) -0.0012 (0.0025)
## PhenoAge EAA 0.0005 * (0.0003) -0.005 (0.0043) -0.0009 (0.0027)
## Skin&Blood EAA 0.0004 (0.0002) 0.0026 (0.0032) 0.0013 (0.0021)
## GrimAge EAA 0.0007 ***(0.0002) 0.0014 (0.003 ) 0.0014 (0.0019)
## DNAmTL 0 (0 ) 0 (0.0002) 0 (0.0001)
## IEAA 0.0006 * (0.0003) -0.0101* (0.004 ) -0.0054* (0.0026)
## EEAA 0.0006 (0.0003) -0.0013 (0.0051) -0.0003 (0.0032)
## <NA> <NA> <NA>
## BbF BkF CHR
## Horvath EAA -0.0033 (0.0029) -0.0192 (0.0133) -0.0033 (0.0032)
## Hannum EAA -0.0015 (0.0026) -0.0069 (0.0116) -0.0015 (0.0028)
## PhenoAge EAA -0.0015 (0.0028) -0.0093 (0.0125) -0.0007 (0.003 )
## Skin&Blood EAA 0.0013 (0.0021) 0.0061 (0.0094) 0.0013 (0.0022)
## GrimAge EAA 0.0013 (0.0019) 0.006 (0.0086) 0.0019 (0.002 )
## DNAmTL 0 (0.0001) 0.0001 (0.0005) 0 (0.0001)
## IEAA -0.0048 (0.0026) -0.0266* (0.0116) -0.0047 (0.0028)
## EEAA -0.0006 (0.0033) -0.0025 (0.0147) -0.0004 (0.0035)
## <NA> <NA> <NA>
## DBA FLT FLU
## Horvath EAA -0.0186 (0.0117) -0.006 (0.0031) 0.0008 (0.0008)
## Hannum EAA -0.0085 (0.0102) -0.0023 (0.0027) -0.0003 (0.0007)
## PhenoAge EAA -0.0082 (0.011 ) -0.0013 (0.0029) 0.0006 (0.0007)
## Skin&Blood EAA 0.0044 (0.0083) -0.0003 (0.0022) 0.0005 (0.0006)
## GrimAge EAA 0.0048 (0.0076) 0.0012 (0.002 ) 0.0009 (0.0005)
## DNAmTL -0.0001 (0.0005) 0.0001 (0.0001) 0 (0 )
## IEAA -0.0262* (0.0102) -0.0064* (0.0027) 0.0006 (0.0007)
## EEAA -0.0047 (0.013 ) -0.0021 (0.0034) -0.0001 (0.0009)
## <NA> <NA> <NA>
## IPY NAP PHE
## Horvath EAA -0.0107 (0.0082) 0.0002 ** (0.0001) 0.0006 (0.0005)
## Hannum EAA -0.0019 (0.0072) 0.0001 (0.0001) -0.0001 (0.0004)
## PhenoAge EAA -0.008 (0.0077) 0.0001 * (0.0001) 0.0004 (0.0005)
## Skin&Blood EAA 0.0055 (0.0058) 0.0001 (0 ) 0.0003 (0.0004)
## GrimAge EAA 0.0042 (0.0053) 0.0001 ***(0 ) 0.0006 * (0.0003)
## DNAmTL 0.0001 (0.0003) 0 (0 ) 0 (0 )
## IEAA -0.017 * (0.0072) 0.0001 * (0.0001) 0.0005 (0.0004)
## EEAA -0.0002 (0.0091) 0.0001 (0.0001) 0 (0.0006)
## <NA> <NA> <NA>
## PYR
## Horvath EAA -0.0054 (0.003 )
## Hannum EAA -0.0018 (0.0026)
## PhenoAge EAA -0.001 (0.0028)
## Skin&Blood EAA 0.0002 (0.0021)
## GrimAge EAA 0.0012 (0.0019)
## DNAmTL 0.0001 (0.0001)
## IEAA -0.006 * (0.0026)
## EEAA -0.0015 (0.0033)
## <NA>Urinary Measurements
## X: Urinary Measurements:## Benzanthracene_Chrysene Naphthalene
## Horvath EAA -0.0347 (0.1329) -0.0015* (0.0006)
## Hannum EAA 0.0524 (0.1142) -0.0012* (0.0005)
## PhenoAge EAA -0.0577 (0.1229) -0.0011 (0.0006)
## Skin&Blood EAA 0.0831 (0.0963) -0.0015***(0.0004)
## GrimAge EAA 0.1139 (0.0848) 0 (0.0004)
## DNAmTL -0.0044 (0.005 ) 0 (0 )
## IEAA -0.1061 (0.1218) -0.001 (0.0005)
## EEAA 0.1062 (0.1448) -0.0012 (0.0007)
## [P<0.001: ***; P<0.01: **; P<0.05: *] <NA>
## 2.Methylnaphthalene 1.Methylnaphthalene Acenaphthene
## Horvath EAA -0.0076 (0.0072) -0.0107 (0.0175) 0.0222 (0.0388)
## Hannum EAA -0.0041 (0.0063) -0.0195 (0.0149) 0.0364 (0.0331)
## PhenoAge EAA -0.009 (0.0067) -0.0197 (0.016 ) 0.0871 * (0.0352)
## Skin&Blood EAA -0.0073 (0.0053) -0.0248 (0.0126) -0.0153 (0.0283)
## GrimAge EAA 0.0074 (0.0047) 0.0115 (0.0112) 0.0632 * (0.0242)
## DNAmTL -0.0003 (0.0003) -0.0006 (0.0007) -0.0012 (0.0015)
## IEAA -0.0049 (0.0067) -0.0035 (0.016 ) 0.0423 (0.0354)
## EEAA -0.0027 (0.0079) -0.0178 (0.019 ) 0.0437 (0.0421)
## <NA> <NA> <NA>
## Phenanthrene_Anthracene Fluoranthene Pyrene
## Horvath EAA 0.0032 * (0.0015) 0.0313 (0.0176) 0.0604 (0.8089)
## Hannum EAA 0 (0.0013) 0.0014 (0.0152) 0.4964 (0.6998)
## PhenoAge EAA 0.0016 (0.0014) 0.0186 (0.0164) 1.1837 (0.7204)
## Skin&Blood EAA 0.0003 (0.0011) 0.0075 (0.013 ) 0.4335 (0.5651)
## GrimAge EAA 0.003 ** (0.0009) 0.0336 ** (0.011 ) 0.8996 (0.5026)
## DNAmTL -0.0002** (0.0001) -0.002 ** (0.0007) -0.0247 (0.0307)
## IEAA 0.0027 (0.0014) 0.0253 (0.0161) 0.3588 (0.7359)
## EEAA 0.0005 (0.0016) 0.0066 (0.0194) 0.7558 (0.8847)
## <NA> <NA> <NA>Current fuel type
In the following section, we performed traditional linear regression with equation \[Y = \beta_0 + \beta_1 * I(\text{Smokeles}) + \beta_2 * I(\text{Smoky}) + \beta_3 * I(\text{Wood_and_or_Plant})\] where \(Y\) is one of the epigenetic age accelerations and the reference as the gas/electricity fuel type from the control group.
The estimations of \(\beta_0\), \(\beta_1\), \(\beta_2\), \(\beta_3\), \(\beta_4\) with given \(Y\) are shown below, which can be interpreted as “the expected change of Y if switching form the gas/electricity fuel type to the given fuel type, while holding other variables constant”.
The numbers of observations with each current fuel type:
##
## Gas/Elect Smokeles Smoky Wood_and_or_Plant
## 12 17 87 8
Childhood Exposure: Birth Fuel Type
In the following section, we performed traditional linear regression with equation \[Y = \beta_0 + \beta_1 * I(Smokeles) + \beta_2 * I(Smoky) + \beta_3 * I(Wood) + \beta_4 * I(Mix)\] where \(Y\) is one of the epigenetic age accelerations and the reference as the gas/electricity fuel type from the control group.
The estimations of \(\beta_0\), \(\beta_1\), \(\beta_2\), \(\beta_3\), and \(\beta_4\) with given \(Y\) are shown below, which can be interpreted as “the expected change of Y if switching form the gas/electricity fuel type to the given fuel type, while holding other variables constant”.
The numbers of observations with each current fuel type:
##
## Gas/Elect Mix Smokeles Smoky Wood
## 12 53 5 47 11
Lifetime Exposure: Cumulative Fuel Type
In the following section, we performed traditional linear regression with equation \[Y = \beta_0 + \beta_1 * I(Smoky) + \beta_2 * I(Mix)\] where \(Y\) is one of the epigenetic age accelerations and the reference as the gas/electricity fuel type from the control group.
The estimations of \(\beta_0\), \(\beta_1\), and \(\beta_2\) with given \(Y\) are shown below, which can be interpreted as “the expected change of Y if switching form the gas/electricity fuel type to the given fuel type, while holding other variables constant”.
The numbers of observations with each cumulative fuel type:
##
## Gas/Elect Mix Smoky
## 12 82 37
Current Stove Type
##
## Firepit_and_unventilated Gas/Elect Mix
## 22 12 19
## Portable_stove Ventilated
## 20 51In the following section, we performed traditional linear regression with equation \[Y = \beta_0 + \beta_1 * I(\text{Portable_stove}) + \beta_2 * I(\text{Ventilated}) + \beta_3 * I(\text{Firepit_and_unventilated}) + \beta_4 * I(\text{Mix})\] where \(Y\) is one of the epigenetic age accelerations and the baseline as the Gas/Elect stove type from the control group.
The estimations of \(\beta_0\), \(\beta_1\), \(\beta_2\), \(\beta_3\), and \(\beta_4\) with given \(Y\) are shown below, which can be interpreted as “the expected change of Y if switching form the Gas/Electricity stove type to the given stove type, while holding other variables constant”.
Linear regression with log transformation
In the following section, we performed traditional regression with equation \[Y = \beta_0 + \beta_1 *log(x)\] where \(Y\) is one of the epigenetic age accelerations, and \(X\) is one of the ambient exposure measurements or the urinary measurements.
The estimations of \(\beta_1\) with given \(Y\) and \(log(X)\) are shown below, which can be interpreted as “the mean of Y changes given a one-unit increase in log(X) while holding other variables constant”.
Ambient Exposure
## X: Ambient Exposure Measurements:## bap pm25
## Horvath EAA -0.1076 (0.3766) 0.4429 (0.5902)
## Hannum EAA -0.2152 (0.3272) -0.1099 (0.507 )
## PhenoAge EAA -0.3256 (0.3523) -0.0291 (0.5488)
## Skin&Blood EAA 0.4187 (0.263 ) -0.0782 (0.4314)
## GrimAge EAA 0.12 (0.2417) 0.4732 (0.3763)
## DNAmTL -0.0021 (0.0145) -0.0225 (0.0225)
## IEAA -0.5106 (0.3316) 0.1967 (0.5418)
## EEAA -0.0601 (0.4147) 0.0686 (0.6445)
## [P<0.001: ***; P<0.01: **; P<0.05: *] <NA>
## ANY BPE BaA
## Horvath EAA 0.7994 (0.4907) -0.0795 (0.3582) -0.0251 (0.3096)
## Hannum EAA 0.3506 (0.4299) -0.2021 (0.3111) -0.1897 (0.2688)
## PhenoAge EAA 0.6353 (0.4466) -0.3914 (0.3343) -0.2167 (0.2899)
## Skin&Blood EAA 0.587 (0.3403) 0.4958 * (0.2487) 0.2756 (0.217 )
## GrimAge EAA 0.5797 (0.2971) 0.1416 (0.2298) 0.0942 (0.1987)
## DNAmTL -0.0032 (0.0178) -0.0053 (0.0138) -0.0013 (0.0119)
## IEAA 0.5578 (0.4315) -0.4463 (0.3159) -0.3353 (0.2735)
## EEAA 0.4099 (0.5422) -0.0977 (0.3943) -0.0628 (0.3408)
## <NA> <NA> <NA>
## BbF BkF CHR
## Horvath EAA 0.0666 (0.3955) -0.092 (0.3903) 0.0732 (0.3155)
## Hannum EAA -0.0909 (0.344 ) -0.1946 (0.3391) -0.1423 (0.2742)
## PhenoAge EAA -0.3042 (0.3702) -0.2683 (0.3655) -0.2478 (0.2953)
## Skin&Blood EAA 0.4133 (0.2765) 0.4052 (0.2729) 0.2033 (0.2218)
## GrimAge EAA 0.0817 (0.254 ) 0.1449 (0.2504) 0.066 (0.2026)
## DNAmTL 0.0002 (0.0152) -0.0003 (0.015 ) 0.0011 (0.0121)
## IEAA -0.3291 (0.3503) -0.4921 (0.3441) -0.25 (0.2796)
## EEAA 0.033 (0.4355) -0.0244 (0.4298) -0.0267 (0.3474)
## <NA> <NA> <NA>
## DBA FLT FLU
## Horvath EAA -0.1919 (0.3165) -0.1098 (0.2381) 0.9256 (0.5483)
## Hannum EAA -0.1881 (0.2753) -0.1805 (0.2067) 0.0906 (0.4827)
## PhenoAge EAA -0.1555 (0.2971) -0.171 (0.2231) 0.4042 (0.5035)
## Skin&Blood EAA 0.27 (0.2223) 0.1043 (0.1678) 0.5336 (0.3829)
## GrimAge EAA 0.1159 (0.2034) 0.0775 (0.1529) 0.4703 (0.3359)
## DNAmTL -0.0105 (0.0121) 0.001 (0.0092) -0.006 (0.0199)
## IEAA -0.5038 (0.278 ) -0.2984 (0.2101) 0.6214 (0.4828)
## EEAA -0.0711 (0.349 ) -0.0818 (0.2623) 0.1179 (0.6085)
## <NA> <NA> <NA>
## IPY NAP PHE
## Horvath EAA -0.2733 (0.3977) 1.3359 * (0.5622) 0.9582 (0.5159)
## Hannum EAA -0.2651 (0.3458) 0.5956 (0.4986) 0.1196 (0.4556)
## PhenoAge EAA -0.3284 (0.3727) 0.9013 (0.5172) 0.5163 (0.4738)
## Skin&Blood EAA 0.407 (0.2786) 0.9097 * (0.3911) 0.519 (0.3612)
## GrimAge EAA 0.1506 (0.2556) 0.7901 * (0.3433) 0.5162 (0.3158)
## DNAmTL -0.0069 (0.0153) -0.0069 (0.0207) -0.0033 (0.0188)
## IEAA -0.6474 (0.3493) 0.9301 (0.4975) 0.6943 (0.454 )
## EEAA -0.166 (0.4384) 0.7714 (0.6282) 0.1681 (0.5742)
## <NA> <NA> <NA>
## PYR
## Horvath EAA -0.0925 (0.24 )
## Hannum EAA -0.1644 (0.2084)
## PhenoAge EAA -0.1787 (0.2248)
## Skin&Blood EAA 0.1355 (0.169 )
## GrimAge EAA 0.0627 (0.1542)
## DNAmTL -0.0001 (0.0092)
## IEAA -0.306 (0.2117)
## EEAA -0.0564 (0.2644)
## <NA>Urinary Measurements
## X: Urine Measurements:## Benzanthracene_Chrysene Naphthalene
## Horvath EAA 0.4364 (0.4199) -0.1112 (0.5242)
## Hannum EAA 0.0504 (0.3625) -0.041 (0.4494)
## PhenoAge EAA -0.235 (0.3897) -0.1722 (0.4862)
## Skin&Blood EAA 0.1857 (0.306 ) -0.2724 (0.3817)
## GrimAge EAA 0.3483 (0.2691) 0.4953 (0.3327)
## DNAmTL -0.0194 (0.0159) -0.0152 (0.02 )
## IEAA -0.1814 (0.3873) 0.1021 (0.4804)
## EEAA 0.2666 (0.4597) 0.0638 (0.5713)
## [P<0.001: ***; P<0.01: **; P<0.05: *] <NA>
## 2.Methylnaphthalene 1.Methylnaphthalene Acenaphthene
## Horvath EAA 0.1993 (0.5128) 0.0692 (0.4838) 0.2138 (0.4341)
## Hannum EAA 0.36 (0.4455) 0.1215 (0.4129) 0.4444 (0.3704)
## PhenoAge EAA -0.0367 (0.4763) -0.1028 (0.4451) 0.9413 * (0.3944)
## Skin&Blood EAA -0.1199 (0.3799) -0.2512 (0.3518) -0.172 (0.3166)
## GrimAge EAA 0.7028 * (0.3315) 0.3109 (0.308 ) 0.6184 * (0.2727)
## DNAmTL -0.0342 (0.0194) -0.0115 (0.0184) -0.0141 (0.0165)
## IEAA 0.1031 (0.4729) -0.1805 (0.441 ) 0.3237 (0.3972)
## EEAA 0.5612 (0.5589) 0.3686 (0.5256) 0.6301 (0.4702)
## <NA> <NA> <NA>
## Phenanthrene_Anthracene Fluoranthene Pyrene
## Horvath EAA 0.8824 * (0.3813) 0.5725 (0.4641) 0.307 (0.7555)
## Hannum EAA 0.2718 (0.3329) 0.1574 (0.4 ) 0.2786 (0.655 )
## PhenoAge EAA 0.5222 (0.3582) 0.5958 (0.4299) 0.6001 (0.6792)
## Skin&Blood EAA 0.1645 (0.2836) -0.0413 (0.3405) 0.6492 (0.5259)
## GrimAge EAA 0.5446 * (0.2445) 0.6226 * (0.2937) 0.5533 (0.4736)
## DNAmTL -0.0413** (0.0144) -0.0394* (0.0175) -0.027 (0.0286)
## IEAA 0.5602 (0.3533) 0.2816 (0.4271) 0.5419 (0.6865)
## EEAA 0.4976 (0.4219) 0.245 (0.5082) 0.5302 (0.828 )
## <NA> <NA> <NA>